An investigation into bacterial water quality problems was conducted on an interconnected stream and irrigation system within the Oldman River Basin of southern Alberta, Canada. Levels of indicator bacteria, including fecal coliforms, generic Escherichia coli and fecal streptococci, were repeatedly measured in streams and irrigation return canals of this river basin during the summer of 2001. Bacterial-loading segments of the irrigation/stream system were identified through a comparison of indicator bacteria levels in pairs of upstream and downstream sites. Mann?Whitney U-tests indicated that reservoirs significantly reduced bacterial counts. A temporal comparison of E. coli counts and river discharges suggested that these indicator bacteria do not originate from within in-stream sediments. Site-specific as well as cumulative inputs from a variety of non-point sources are likely to be responsible for the high downstream levels of indicator bacteria in this water system. The use of management practices such as in-stream reservoirs may significantly reduce contamination, and increase the quality of limited rural water supplies to allow their reuse and safe discharge into downstream water sources. The identification of bacteria-loading river/canal segments could also be used to prioritize restoration projects.